The AFL announced an inquiry into the structure of the sport following the surprise departure of long-serving chief executive officer of the Victorian Country Football League Glenn Scott on Monday afternoon.

AFL chief executive officer Andrew Demetriou released a statement on Tuesday saying he was "alarmed" to learn that Mr Scott, who he called "one of football's most effective and respected administrators", had resigned after nine years in the position.

VCFL president Nicholas Rolfe was notified hours before the announcement of a review which will be led by AFL Victoria chairman and former chief executive of the Essendon Football Club, Peter Jackson.

"On behalf of the AFL we're all pretty disappointed that we lose a guy like this, and perhaps in such a sudden way as well and we'd like to understand a bit more about it," Mr Jackson said.

"We thought consultation would be a fair enough request."

Mr Jackson said the inquiry was not centred on the departure of Mr Scott but admitted it was a catalyst which has led to an "overdue review."

"It's not a review into Glenn Scott's resignation or the factor's causing that, it's actually a review into the structure and what's the best structure for football in country Victoria."

Mr Jackson said he could not comment on speculation of ongoing tension between Mr Scott and VCFL's board of directors.

The VCFL announced Steven Reaper had been appointed to the succeed Mr Scott at the same time it announced his resignation.

Mr Rolfe denied any tensions between Mr Scott and the VCFL but would not comment into the circumstances surround his resignation on Monday afternoon.

"Ordinarily in the past we have not discussed staff issues with AFL Victoria and as president I was unaware that we were required to do that," Mr Rolfe said.

"We would be looking at achieving a positive result out of this, as Peter (Jackson) seems to be putting a positive spin, I would be putting a positive spin on it as well and if you read the press release from Andrew (Demetriou) it talks very positively about country football and in one view that it's never been in a better condition."

Mr Jackson said he planned to organise a meeting between with "key country football stakeholders" in the coming weeks.